Sodium in the structure of Ternary Complex of Human Dna Polymerase Beta With An Abasic Site (Thf): Dapcpp Mismatch (pdb 3isd)

The binding sites of Sodium atom in the structure of Ternary Complex of Human Dna Polymerase Beta With An Abasic Site (Thf): Dapcpp Mismatch (pdb code 3isd). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3isd structure was solved by W.A.BEARD, D.D.SHOCK, V.K.BATRA, L.C.PEDERSEN, S.H.WILSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 21.2-2.6 Space group P1211 a (A) 54.700 b (A) 77.640 c (A) 55.220 alpha (°) 90.00 beta (°) 113.67 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 26.2 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3isd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3isd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, A: Gly107, P: Dc8, P: Dg9, A: Hoh377, A: Hoh494, P: Hoh36, conact list: Atom Atom Distance (A) Na O A:Leu100 4.64 Na O A:Thr101 2.12 Na N A:Thr101 4.98 Na CB A:Thr101 4.30 Na C A:Thr101 3.12 Na CA A:Thr101 3.71 Na O A:Arg102 4.68 Na N A:Arg102 4.20 Na C A:Arg102 4.20 Na CA A:Arg102 4.53 Na O A:Val103 2.57 Na N A:Val103 4.01 Na C A:Val103 3.38 Na CA A:Val103 4.36 Na N A:Ser104 3.97 Na C A:Ser104 4.51 Na CA A:Ser104 3.95 Na N A:Gly105 4.23 Na O A:Ile106 2.55 Na N A:Ile106 4.05 Na CB A:Ile106 4.76 Na C A:Ile106 3.61 Na CA A:Ile106 4.34 Na N A:Gly107 4.57 Na CA A:Gly107 4.77 Na O3' P:Dc8 4.81 Na OP1 P:Dg9 2.64 Na P P:Dg9 3.60 Na OP2 P:Dg9 3.67 Na O5' P:Dg9 4.54 Na O A:Hoh377 2.57 Na O A:Hoh494 3.65 Na O P:Hoh36 2.62 interactive model: Sodium binding site 2 out of 3 in 3isd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3isd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala59, A: Lys60, A: Lys61, A: Leu62, A: Pro63, A: Gly64, A: Val65, A: Gly66, D: Dt2, D: Dc3, D: Hoh6, conact list: Atom Atom Distance (A) Na O A:Ala59 4.73 Na O A:Lys60 2.43 Na CE A:Lys60 4.92 Na CD A:Lys60 4.66 Na C A:Lys60 3.48 Na CA A:Lys60 4.41 Na O A:Lys61 3.70 Na N A:Lys61 4.28 Na C A:Lys61 3.56 Na CA A:Lys61 4.29 Na O A:Leu62 2.03 Na N A:Leu62 3.52 Na CB A:Leu62 4.82 Na C A:Leu62 2.78 Na CA A:Leu62 3.69 Na N A:Pro63 3.50 Na CB A:Pro63 4.96 Na CD A:Pro63 4.79 Na C A:Pro63 4.40 Na CA A:Pro63 3.71 Na N A:Gly64 4.21 Na O A:Val65 2.95 Na N A:Val65 4.12 Na CB A:Val65 4.55 Na C A:Val65 3.92 Na CA A:Val65 4.42 Na N A:Gly66 4.97 Na O3' D:Dt2 4.92 Na OP1 D:Dc3 2.60 Na P D:Dc3 3.95 Na OP2 D:Dc3 4.47 Na O5' D:Dc3 4.86 Na O D:Hoh6 2.73 interactive model: Sodium binding site 3 out of 3 in 3isd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3isd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: Dt3, P: Dg4, P: Da5, P: Hoh56, P: Hoh184, conact list: Atom Atom Distance (A) Na C2' P:Dt3 4.12 Na C8 P:Dg4 3.82 Na C6 P:Dg4 4.21 Na C5 P:Dg4 3.86 Na N7 P:Dg4 2.88 Na O6 P:Dg4 3.81 Na N6 P:Da5 4.23 Na O P:Hoh56 2.89 Na O P:Hoh184 2.47 interactive model: